SMTL ID : 8css.1

Human mitochondrial small subunit assembly intermediate (State D)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 9 residues within 4Å: Chain F: H.303, M.307, P.332, C.333, H.335, C.339, P.340, C.347, C.404 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.333, F:C.339, F:C.347, F:C.404

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.2: 13 residues within 4Å: Chain F: Y.158, F.192, G.193, G.195, T.196, S.198, D.218, R.219, S.220, M.223, A.265, F.266, L.271 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:Y.158 Hydrogen bonds: F:Y.158, F:G.193, F:G.195, F:S.198, F:S.198, F:D.218, F:R.219, F:S.220 Salt bridges: F:D.218

7 x K: POTASSIUM ION(Non-functional Binders)(Non-covalent)

K.3: 4 residues within 4Å: Chain H: C.55, C.60, C.61, C.195 No protein-ligand interaction detected (PLIP) K.4: 4 residues within 4Å: Chain H: G.70, A.71, G.72, G.144 No protein-ligand interaction detected (PLIP) K.5: 4 residues within 4Å: Chain H: C.243, G.254 Chain Q: P.73, N.74 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:P.73 K.6: 4 residues within 4Å: Chain H: C.458, U.460, U.945, U.946 No protein-ligand interaction detected (PLIP) K.7: 5 residues within 4Å: Chain H: C.153, A.154, C.158, C.159 Ligands: MG.20 No protein-ligand interaction detected (PLIP) K.8: 4 residues within 4Å: Chain H: C.188, U.191, A.192, U.203 No protein-ligand interaction detected (PLIP) K.9: 4 residues within 4Å: Chain H: U.241, G.242, C.257, A.258 No protein-ligand interaction detected (PLIP)

32 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.10: 2 residues within 4Å: Chain H: A.110 Ligands: NAD.40 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain H: A.399, G.487 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain H: G.445 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain H: A.71, G.72, G.144 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain H: U.290, A.291, A.292, A.293 No protein-ligand interaction detected (PLIP) MG.15: 1 residues within 4Å: Chain H: G.381 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain H: A.407, C.452 No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Chain H: G.398 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain H: U.300, G.398 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain H: U.8, U.9 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain H: A.154, C.159 Ligands: K.7 No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain H: A.46, C.168, A.169 No protein-ligand interaction detected (PLIP) MG.22: 4 residues within 4Å: Chain H: G.231, C.233, A.234, A.235 No protein-ligand interaction detected (PLIP) MG.23: 5 residues within 4Å: Chain H: G.6, U.7, A.16, G.17, C.18 No protein-ligand interaction detected (PLIP) MG.24: 4 residues within 4Å: Chain H: U.26, U.27, A.180, C.181 No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Chain H: A.84 No protein-ligand interaction detected (PLIP) MG.26: 1 residues within 4Å: Chain H: A.99 No protein-ligand interaction detected (PLIP) MG.27: 2 residues within 4Å: Chain H: U.111, C.499 No protein-ligand interaction detected (PLIP) MG.28: 2 residues within 4Å: Chain H: C.171, G.173 No protein-ligand interaction detected (PLIP) MG.29: 1 residues within 4Å: Chain H: C.261 No protein-ligand interaction detected (PLIP) MG.30: 5 residues within 4Å: Chain H: A.28, G.29, C.30, G.273, U.274 No protein-ligand interaction detected (PLIP) MG.31: 2 residues within 4Å: Chain H: A.400 Ligands: NAD.40 No protein-ligand interaction detected (PLIP) MG.32: 1 residues within 4Å: Chain H: A.492 No protein-ligand interaction detected (PLIP) MG.33: 2 residues within 4Å: Chain H: U.497, A.498 No protein-ligand interaction detected (PLIP) MG.34: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.35: 4 residues within 4Å: Chain H: G.294, A.295, U.297, C.461 No protein-ligand interaction detected (PLIP) MG.36: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.37: 3 residues within 4Å: Chain H: U.612, G.680, G.681 No protein-ligand interaction detected (PLIP) MG.38: 4 residues within 4Å: Chain H: C.569, G.570, A.706, A.707 No protein-ligand interaction detected (PLIP) MG.39: 5 residues within 4Å: Chain H: G.929, U.930, A.931, U.940, G.941 No protein-ligand interaction detected (PLIP) MG.41: 4 residues within 4Å: Chain I: H.93, D.224, D.240, D.241 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:H.93, I:D.224, I:D.240, I:D.241 MG.46: 2 residues within 4Å: Chain 4: T.135 Ligands: ATP.45 3 PLIP interactions: 1 interactions with chain 4, 2 Ligand-Water interactions Metal complexes: 4:T.135, H2O.4, H2O.4

1 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.40: 16 residues within 4Å: Chain H: A.134, A.135, A.136, U.301, U.302, G.398, A.399, A.400, C.401 Chain Q: R.38 Chain S: L.194, Y.195, Y.196, R.197 Ligands: MG.10, MG.31 3 PLIP interactions: 2 interactions with chain Q, 1 interactions with chain S Water bridges: Q:R.38 Salt bridges: Q:R.38 Hydrogen bonds: S:Y.196

1 x ZN: ZINC ION(Non-covalent)

ZN.42: 5 residues within 4Å: Chain V: C.94, C.105, C.108, C.143, Q.146 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:C.94, V:C.105, V:C.108, V:C.143

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.43: 6 residues within 4Å: Chain L: C.105, I.108 Chain W: C.65, C.68, C.100, K.103 4 PLIP interactions: 3 interactions with chain W, 1 interactions with chain L, Metal complexes: W:C.65, W:C.68, W:C.100, L:C.105 FES.44: 5 residues within 4Å: Chain 0: C.139, C.141, C.149 Chain T: C.26, R.29 4 PLIP interactions: 3 interactions with chain 0, 1 interactions with chain T, Metal complexes: 0:C.139, 0:C.141, 0:C.149, T:C.26

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.45: 18 residues within 4Å: Chain 4: P.84, L.99, M.100, R.102, K.130, G.131, T.132, G.133, K.134, T.135, L.136, S.311, T.313, Y.348, P.388, S.389, E.392 Ligands: MG.46 17 PLIP interactions: 17 interactions with chain 4 Hydrogen bonds: 4:M.100, 4:M.100, 4:R.102, 4:G.131, 4:T.132, 4:T.132, 4:G.133, 4:K.134, 4:T.135, 4:T.135, 4:L.136, 4:S.311, 4:T.313, 4:T.313, 4:E.392 Salt bridges: 4:K.134, 4:K.134

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.47: 11 residues within 4Å: Chain 4: Y.173, R.177, Y.208, V.209, W.210, D.238, G.241, I.242, K.245, N.292, K.295 12 PLIP interactions: 12 interactions with chain 4 Hydrogen bonds: 4:Y.173, 4:R.177, 4:V.209, 4:V.209, 4:N.292 Salt bridges: 4:R.177, 4:D.238, 4:K.245, 4:K.295, 4:K.295 pi-Stacking: 4:Y.173, 4:Y.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harper, N.J. et al., Principles of mitoribosomal small subunit assembly in eukaryotes. Nature (2023)

Release Date

2022-12-14

Peptides

28S ribosomal protein S34, mitochondrial: A
28S ribosomal protein S35, mitochondrial: B
Aurora kinase A-interacting protein: C
Pentatricopeptide repeat domain-containing protein 3, mitochondrial: D
Putative ribosome-binding factor A, mitochondrial: E
Methyltransferase-like protein 17, mitochondrial: F
Malonyl-CoA-acyl carrier protein transacylase, mitochondrial: G
28S ribosomal protein S2, mitochondrial: I
28S ribosomal protein S24, mitochondrial: J
28S ribosomal protein S5, mitochondrial: K
28S ribosomal protein S6, mitochondrial: L
28S ribosomal protein S7, mitochondrial: M
28S ribosomal protein S9, mitochondrial: N
28S ribosomal protein S10, mitochondrial: O
28S ribosomal protein S11, mitochondrial: P
28S ribosomal protein S12, mitochondrial: Q
28S ribosomal protein S14, mitochondrial: R
28S ribosomal protein S15, mitochondrial: S
28S ribosomal protein S16, mitochondrial: T
28S ribosomal protein S17, mitochondrial: U
28S ribosomal protein S18b, mitochondrial: V
28S ribosomal protein S18c, mitochondrial: W
28S ribosomal protein S21, mitochondrial: X
28S ribosomal protein S22, mitochondrial: Y
28S ribosomal protein S23, mitochondrial: Z
28S ribosomal protein S25, mitochondrial: 0
28S ribosomal protein S26, mitochondrial: 1
28S ribosomal protein S27, mitochondrial: 2
28S ribosomal protein S28, mitochondrial: 3
28S ribosomal protein S29, mitochondrial: 4
28S ribosomal protein S31, mitochondrial: 5
28S ribosomal protein S33, mitochondrial: 6

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
0

B
1

C
3

D
4

E
6

F
7

G
8

I
B

J
C

K
D

L
E

M
F

N
G

O
H

P
I

Q
J

R
K

S
L

T
M

U
N

V
O

W
P

X
Q

Y
R

Z
S

0
T

1
U

2
V

3
W

4
X

5
Y

6
Z

28S ribosomal protein S34, mitochondrial

28S ribosomal protein S35, mitochondrial

Aurora kinase A-interacting protein

Pentatricopeptide repeat domain-containing protein 3, mitochondrial

Putative ribosome-binding factor A, mitochondrial

Methyltransferase-like protein 17, mitochondrial

Malonyl-CoA-acyl carrier protein transacylase, mitochondrial

28S ribosomal protein S2, mitochondrial

28S ribosomal protein S24, mitochondrial

28S ribosomal protein S5, mitochondrial

28S ribosomal protein S6, mitochondrial

28S ribosomal protein S7, mitochondrial

28S ribosomal protein S9, mitochondrial

28S ribosomal protein S10, mitochondrial

28S ribosomal protein S11, mitochondrial

28S ribosomal protein S12, mitochondrial

28S ribosomal protein S14, mitochondrial

28S ribosomal protein S15, mitochondrial

28S ribosomal protein S16, mitochondrial

28S ribosomal protein S17, mitochondrial

28S ribosomal protein S18b, mitochondrial

28S ribosomal protein S18c, mitochondrial

28S ribosomal protein S21, mitochondrial

28S ribosomal protein S22, mitochondrial

28S ribosomal protein S23, mitochondrial

28S ribosomal protein S25, mitochondrial

28S ribosomal protein S26, mitochondrial

28S ribosomal protein S27, mitochondrial

28S ribosomal protein S28, mitochondrial

28S ribosomal protein S29, mitochondrial

28S ribosomal protein S31, mitochondrial

28S ribosomal protein S33, mitochondrial

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